Best would be to cut a hole in the car and feed the coax through that. There are antenna mounts designed to bolt to a car body panel and take care of structurally supporting the antenna and forming a weatherproof seal. NMO mounts are pretty common for VHF antennas.
If you don't want to modify your car in any way, use a section of small diameter coax to slip through the rubber seal around a door or trunk if your feedline is too fat. You can use small connectors like SMA to connect it to your feedline. Just be sure the connections are appropriately weatherproofed to avoid getting water in the feedline.